Showing : featureCounts • reset
3
votes
4
replies
356
views
Clarification on counting in Rsubread (featureCounts)
featureCounts Rsubread
updated 8 days ago by 53k • written 5 weeks ago by • 0
0
votes
0
replies
330
views
Blank gene_id in featureCounts
featureCounts Rsubread
8 months ago Meg • 0
5
votes
10
replies
2.7k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 13 months ago by • 0
0
votes
1
reply
1.1k
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 11 months ago by 53k • written 11 months ago by ▴ 80
0
votes
1
reply
962
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 13 months ago by 53k • written 22 months ago by • 0
1
vote
3
replies
2.1k
views
featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
15 months ago yasmin.hilliam ▴ 10
0
votes
1
reply
770
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
15 months ago isaac.vock • 0
6
votes
5
replies
4.6k
views
What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 12 months ago by ▴ 20 • written 17 months ago by • 0
0
votes
4
replies
1.3k
views
featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts Subread Bioconductor
18 months ago • updated 17 months ago Jessica • 0
1
vote
2
replies
1.0k
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
17 months ago Anke • 0
4
votes
2
replies
2.3k
views
Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor featurecounts subread
19 months ago Rachael • 0
2
votes
4
replies
1.7k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
22 months ago • updated 19 months ago isaac.vock • 0
1
vote
1
reply
1.2k
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 22 months ago by ★ 3.6k • written 23 months ago by • 0
7
votes
28
replies
8.9k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 23 months ago by 53k • written 10.9 years ago by ★ 7.9k
0
votes
4
replies
1.6k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 24 months ago by 53k • written 24 months ago by • 0
4
votes
6
replies
1.7k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
24 months ago isaac.vock • 0
0
votes
2
replies
5.2k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 5.5 years ago by ▴ 80
0
votes
0
replies
2.2k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
2.4 years ago Gordon Smyth 53k
0
votes
2
replies
2.6k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
1
vote
1
reply
1.3k
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 2.5 years ago by ▴ 450 • written 2.5 years ago by • 0
0
votes
1
reply
1.7k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 2.7 years ago by ★ 3.6k • written 2.7 years ago by • 0
0
votes
0
replies
864
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
2.8 years ago barrypraveen • 0
2
votes
9
replies
3.6k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
2.9 years ago Hilary ▴ 40
0
votes
2
replies
1.5k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 2.9 years ago by ★ 3.6k • written 3.1 years ago by • 0
0
votes
0
replies
1.2k
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
2.9 years ago yao hua • 0
0
votes
1
reply
1.6k
views
Subread installation on Linux ARM64
subread featureCounts
updated 3.0 years ago by ▴ 450 • written 3.0 years ago by • 0
0
votes
1
reply
1.2k
views
DEG analysis with Paired-end RNA-seq data using DESeq2, do I need to contain the library type when I using DESeq() function if I already using featur…
DESeq2 featurecounts
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by • 0
3
votes
3
replies
7.2k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
0
votes
1
reply
4.0k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 3.1 years ago by ★ 1.4k • written 3.1 years ago by • 0
1
vote
1
reply
4.0k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
0
votes
0
replies
1.1k
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
2
votes
3
replies
2.5k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
2
votes
2
replies
1.4k
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
3.3 years ago dario.beraldi • 0
0
votes
0
replies
1.0k
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3.3 years ago rridley3 • 0
0
votes
2
replies
2.7k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
3.4 years ago KMS ▴ 20
0
votes
1
reply
5.4k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
0
votes
1
reply
1.3k
views
fetaure counts err
featurecounts
updated 3.5 years ago by ★ 3.6k • written 3.6 years ago by • 0
0
votes
1
reply
1.5k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
3.7 years ago • updated 3.6 years ago NIK • 0
1
vote
1
reply
2.3k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
2
votes
1
reply
2.4k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 3.7 years ago by ★ 1.4k • written 3.7 years ago by ▴ 10
0
votes
4
replies
2.7k
views
featureCounts: 0% successfully assigned fragments
featureCounts
3.7 years ago KMS ▴ 20
1
vote
4
replies
2.5k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
3.7 years ago Chise ▴ 10
3
votes
11
replies
5.9k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
3.8 years ago • updated 3.7 years ago Sarah_piggy ▴ 10
1
vote
4
replies
3.1k
views
Subread installation
subread featureCounts
3.8 years ago Lucy ▴ 60
1
vote
5
replies
3.5k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
4.0 years ago • updated 3.9 years ago Lucy ▴ 60
2
votes
2
replies
8.6k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
4.1 years ago Chise ▴ 10
4
votes
4
replies
6.9k
views
FeatureCounts
counts subread RNASeq featurecounts
4.2 years ago k___ ▴ 30
0
votes
2
replies
2.2k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 3.3 years ago by • 0 • written 4.4 years ago by • 0
1
vote
1
reply
1.9k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 4.5 years ago by ★ 3.6k • written 4.5 years ago by • 0
1
vote
5
replies
7.6k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 2.5 years ago by ▴ 450 • written 4.6 years ago by ▴ 10
137 results • Page 1 of 3
Recent ...
Replies
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Awards • All
Popular Question to ATpoint ★ 5.0k
Popular Question to Martin Morgan 25k
Teacher to Michael Love 43k
Popular Question to A • 0
Popular Question to Lluís Revilla Sancho ▴ 760
Locations • All
United States, 4 minutes ago
Poland, 10 minutes ago
Barcelona, Spain, 28 minutes ago
United States, 35 minutes ago
Germany, 42 minutes ago
Traffic: 1550 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6